Fig. 2

NEUROD2 binds to E-box elements proximal to TSSs in vivo. a NEUROD2 consensus sequence was predicted using 32,367 peak regions as input for the MEME-ChIP suite [23]. b Among the 32,367 NEUROD2 peaks, approximately 45 % mapped onto Ensembl annotated genes (mm10 reference genome) [24, 55]. Among them approximately 83 % mapped onto introns, and 17 % to either 5′UTR, CDS or 3′UTR exons. c The binding preference of NEUROD2 to introns, 5′UTR exons, 3′UTR exons and CDS exons was calculated. The number of NEUROD2 binding sites observed on introns (red), 5′UTR (green), 3′UTR (blue) and CDS (purple) exons were normalized to the length of each of these gene segments and compared to a random distribution profile (grey bar). The data suggests approximately an 8-fold enrichment in NEUROD2 binding to the first 5′UTR exon, a 5-fold enrichment in binding to the first CDS exon and approximately 2-fold enrichment in binding to the first and second 3′UTR exons. ***p-value ~ 0, *p-value < 0.001. d A binding map of NEUROD2 relative to closest TSSs, revealed that NEUROD2 has a binding preference within +/− 1000 bps of TSSs. Peaks that mapped upstream (blue) and downstream (red) of TSSs are color-coded. e The distribution profiles of ClosestGene scores [29] calculated by using NEUROD2 peaks (blue) were very significantly different from those calculated using randomly distributed peaks (red) on the genome (***p-value ~ 0). f Distribution of normalized scores for individual genes were generated by subtracting the ClosestGene score calculated using NEUROD2 peaks from that of random peaks. Dark green represents genes whose scores were greater than one standard deviation (σ) above the mean and were used for further analyses